<tool id="make_phylogeny" name="make_phylogeny" version="2.0.0">
 <description>Make Phylogeny</description>
 <requirements>
  <requirement type="binary">make_phylogeny.py</requirement>
 </requirements>
 <command interpreter="python">
 qiime_wrapper.py
 --galaxy_inputdir='$__new_file_path__'
 --galaxy_ext_change='$input_fp'
 --galaxy_new_ext='fasta'
 make_phylogeny.py
 --input_fp='$__new_file_path__'/temporary.fasta
 --tree_method=$tree_method
 --result_fp=$result_fp
 --log_fp=$log_fp
 --root_method=$root_method</command>
 <inputs>
  <param name="input_fp" type="data" format="align" label="input_fp"
   help="Path to read input alignment (output from filter_alignment) [REQUIRED]"/>
  <param name="tree_method" type="select" label="tree_method"
   help="Method for tree building. [default: fasttree]">
    <option value="clearcut">clearcut</option>
    <option value="clustalw">clustalw</option>
    <option value="raxml">raxml</option>
    <option value="fasttree_v1">fasttree_v1</option>
    <option value="fasttree" selected="true">fasttree</option>
    <option value="muscle">muscle</option>
  </param>
  <param name="root_method" type="select" label="root_method"
   help="method for choosing root of phylo tree [default: tree_method_default]">
    <option value="tree_method_default" selected="true">tree_method_default</option>
    <option value="midpoint">midpoint</option>
  </param>
 </inputs>
 <outputs>
  <data format="tre" name="result_fp" label="${tool.name} on ${on_string}: tree" />
  <data format="txt" name="log_fp" label="${tool.name} on ${on_string}: log" />
 </outputs>
 <tests>
 </tests>
 <help>For more information, see make_phylogeny_ in the Qiime documentation.

Updated and validated 01/16/12 by Amanda Zuzolo, Microbiome Analysis Center, George Mason University, Fairfax, VA

Qiime integration courtesy Jim Johnson, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN

.. _make_phylogeny: http://qiime.org/scripts/make_phylogeny.html</help>
</tool>